Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PARP1

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293T_ChIP
strain
HEK293T
tissue
kidney
age
embryo
genotype
wild type
chip antibody
anti-PARP1 antibody (Active Motif; lot# 00909001; catalog# 39561)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody using MAGnify™ Chromatin Immunoprecipitation System (Invitrogen). chip antibody: PARP1; chip antibody vendor: Active Motive; chip antibody lot#: 00909001; chip antibody catalog#: 39561. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 -400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
8763518
Reads aligned (%)
42.3
Duplicates removed (%)
76.6
Number of peaks
85 (qval < 1E-05)

hg38

Number of total reads
8763518
Reads aligned (%)
43.5
Duplicates removed (%)
76.2
Number of peaks
114 (qval < 1E-05)

Base call quality data from DBCLS SRA